The German government has ordered the local station chief of the CIA to leave the country immediately – after a second German government official was arrested in an investigation into US surveillance on its erstwhile ally.

"The representative of the US intelligence services at the embassy of the United States of America has been told to leave Germany," said government spokesman Steffen Seibert, the BBC reports.

The German government took the matter very seriously, Seibert said, and added that while the relationship between his country and the US was important to both parties, any dealings must take place with "mutual trust and openness."

In June the German parliament launched an investigation into US surveillance within the country, a move prompted by leaks from NSA whistleblower Edward Snowden. On July 4, a member of the German security agency was arrested and five days later a member of the state's defense department was also cuffed by cops.

The news of internal spying has caused outrage among the German public and placed relationships between the US and its ally under great strain. German chancellor Angela Merkel said spying on Germany was a "waste of energy."

"In the Cold War maybe there was general mistrust. Today we are living in the 21st Century. Today there are completely new threats," she said.

White House press secretary Josh Earnest told reporters on Thursday that President Obama and Chancellor Merkel had discussed the matter by telephone last week just before the first German arrest and are in fairly frequent contact.

"I’m still able to say that there is an important, functioning national security relationship and intelligence-sharing relationship between the United States and Germany," he said.

"And the reason that that relationship persists is because it is so important to the national security of Germany and to the national security of the United States." ®